Mercurial > repos > greg > vsnp_build_tables
changeset 10:14384fd2a7e2 draft
Uploaded
author | greg |
---|---|
date | Thu, 29 Jul 2021 15:02:47 +0000 |
parents | f641e52353e8 |
children | be32fbc45ae8 |
files | .shed.yml static/images/._table_description.png vsnp_build_tables.xml |
diffstat | 3 files changed, 20 insertions(+), 9 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Jul 29 15:02:47 2021 +0000 @@ -0,0 +1,11 @@ +name: vsnp_build_tables +owner: greg +description: | + Contains a tool that produces Excel spreadsheets from outputs produced by the vsnp_get_snps tool. +homepage_url: https://github.com/USDA-VS/vSNP +long_description: | + Contains a tool that produces Excel spreadsheets from outputs produced by the vsnp_get_snps tool. +remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/sequence_analysis/vsnp/vsnp_build_tables +type: unrestricted +categories: + - Sequence Analysis
--- a/vsnp_build_tables.xml Thu Jul 29 13:52:48 2021 +0000 +++ b/vsnp_build_tables.xml Thu Jul 29 15:02:47 2021 +0000 @@ -22,17 +22,17 @@ mkdir $input_json_dir && #for $i in $input_type_cond.input_avg_mq_json_collection: #set file_name = $i.file_name - #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) + #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s '$file_name' '$input_json_avg_mq_dir/$identifier' && #end for #for $i in $input_type_cond.input_snps_json_collection: #set file_name = $i.file_name - #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) + #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s '$file_name' '$input_json_dir/$identifier' && #end for #for $i in $input_type_cond.input_newick_collection: #set file_name = $i.file_name - #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier)) + #set identifier = re.sub('[^\s\w\-\\.]', '_', str($i.element_identifier)) ln -s '$file_name' '$input_newick_dir/$identifier' && #end for #end if @@ -139,12 +139,12 @@ </param> <param name="gbk_param" value="no"/> <output_collection name="excel" type="list" count="6"> - <element name="Mbovis-01D6_snps_newick_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/> - <element name="Mbovis-01D6_snps_newick_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/> - <element name="Mbovis-01D_snps_newick_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/> - <element name="Mbovis-01D_snps_newick_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/> - <element name="Mbovis-01_snps_newick_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/> - <element name="Mbovis-01_snps_newick_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/> + <element name="Mbovis-01D6_snps_cascade_table" file="Mbovis-01D6_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/> + <element name="Mbovis-01D6_snps_sort_table" file="Mbovis-01D6_sort_table.xlsx" ftype="xlsx" compare="sim_size"/> + <element name="Mbovis-01D_snps_cascade_table" file="Mbovis-01D_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/> + <element name="Mbovis-01D_snps_sort_table" file="Mbovis-01D_sort_table.xlsx" ftype="xlsx" compare="sim_size"/> + <element name="Mbovis-01_snps_cascade_table" file="Mbovis-01_cascade_table.xlsx" ftype="xlsx" compare="sim_size"/> + <element name="Mbovis-01_snps_sort_table" file="Mbovis-01_sort_table.xlsx" ftype="xlsx" compare="sim_size"/> </output_collection> </test> </tests>